1: Do resources have to go back to the capital providence or just a factory to go into the national pool? 2: Can they be transported by rail part way then by transport? 3: I take it they don't take any 'transport' room when going back to the factories right? 4: Can they go overland for a territory or two then to a transport?

A transport chain will act just like a rail network and allow linking back to Japan. Any mix of the two will work and no it doesn't use up room on either network to move them. To answer question 1 in more detail I will provide a typical case. Assume you are playing the western Allies. Your link around Africa has been broken by U-boats and Japan has cleaned out the transports around Australia as well. In this way India is cut off from Washington. The resources from eastern Africa that are still connected to India will flow to India. However, that will be way more then the factories in India needs and they will most likely get wasted. When you mouse over an area you can see how many resources are stored there. An area with 1 resource can hold up to 3 in reserve. Any more collected after that are lost. Say for instance Italy for 1 turn does not link a transport to Sardinia. Sardinia will then store that resource so that it is not lost. As long as Italy moves a transport back to connect it again before it begins to overfill at 3 then you will not have lost that resource production. Just learn to watch them numbers and it will make sense. Another thing there will be overfilling for the western Allies in the either turns of the game because the world produces way more than the Allies have in factory production so there will be many areas that hit the storage limit and then begin to waste the extra produced each turn. Later when the US is really ramped up them reserves will deplete fast and you will need to connect to everywhere you can otherwise not all your factories will produce.

Another thing that comes to mind that new players may not understand. You may have observed, or will observe, that when you are in the western Allied production phase you may see something like a total of 100 resource points available but then when you select England or the US to build from that available number drops. Why is that? Well that is the hint that tells you a large pool of resorces is isolated in either India or Australia. That pool is more than the factories in either of those places need but can't get back to the US to help all of it's factories produce. That is why the Axis hunt down transports. Not only does it directly hurt the Allies by destroying transports that have to be rebuilt, but also kills potential production as well. A two edged sword. That is why a very successful U-boat campaign can really bite the Allies in the ass.